Iran's president Hassan Rouhani made good on his election promise to engage constructively with the outside world. Photograph: Mohammad Berno/AP

It is always hard to predict how historians will judge current events. But the rough draft for any future tally of the Middle East in 2013 must include the Geneva agreement on Iran's nuclear programme, the bloody and escalating war in Syria – and fading hopes for a happy end to the other Arab spring uprisings.

Hassan Rouhani's election as Iranian president in June started a process which led to November's landmark deal with the US and five other countries. That offered relief from crippling economic sanctions in return for a reduction in the uranium enrichment that fuelled suspicions of Iran's ambitions (which it denies) to acquire nuclear weapons.

It is an interim agreement and faces opposition from hardliners in Tehran who mistrust the emollient Rouhani, Republicans in Washington and hawks in Jerusalem, where Israel – anxious to maintain its monopoly of (undeclared) nuclear weapons – was ignored by Barack Obama. If successful, it will end the risk of a pre-emptive Israeli or US attack. But beyond that lies an even bigger prize – an easing of three decades of hostility between Washington and Tehran following the 1979 Islamic revolution – though other disagreements will be difficult to reconcile if a much-vaunted "grand bargain" is to be struck between these old enemies.

Iran's role in Syria is one of those. Tehran has been a loyal supporter of Bashar al-Assad since the uprising erupted in March 2011 – and remains so, with the death toll now estimated at more than 126,000. Evidence of the presence of Iranian revolutionary guards in Syria is unequivocal. The Lebanese Shia movement Hezbollah, which has a close relationship with Iran, has also been fighting openly alongside Assad and resisting Salafi and jihadi groups, including the al-Qaida-linked Jabhat al-Nusra and the Islamic State in Iraq and Syria, which play an increasingly dominant role in the rebel camp.

Iraqi Shia groups have pitched in, and Saudi support for Sunni Islamists fighting al-Qaida has been stepped up as Riyadh has expressed anger and frustration at Obama's policies on Syria and Iran.

A survivor from a chemical weapons attack rests inside a mosque near Damascus. The August attack (widely blamed on the regime, though denied by it) paved the way for the US-Russian deal on disarming Syria's chemical arsenal. Photograph: Reuters

Escalating extremism in Syria ensured that talk of western intervention died away in favour of a strategy of containing rather than resolving the crisis. The August chemical weapons attack near Damascus (widely blamed on the regime, though denied by it) paved the way for the US-Russian deal on disarming Syria's chemical arsenal. That ended the threat of US-led punitive action, already weakened by the dramatic "no" vote in the UK parliament.

It is hard to imagine that the Geneva II peace conference, scheduled for January, will be able to square the same circle that confounded the first Geneva get-together in June 2012. Syria's fragmented opposition demands that Assad step down or negotiate a transfer of power; Assad, emboldened by battlefield successes and the support of Tehran and Moscow, insists he will do no such thing. Assad may well hang on – and even be re-elected in 2014 – but Syria is already divided, with swaths of the north controlled by jihadi groups while the Kurds enjoy de facto autonomy. Talk is rife of the unravelling of the 1916 Sykes-Picot agreement, which carved up the Ottoman empire into spheres of British and French influence after the first world war.

Iraq itself bears the scars of regular suicide bombings targeting civilians and the authority of Nouri al-Maliki's autocratic Shia-dominated government. Violence has escalated since an army raid on a Sunni anti-government protest camp in April.

Egypt suffered a year of turbulence, with 2,000 killed in the mass protests that followed the overthrow of President Mohamed Morsi by the army. The 30 June coup commanded huge popular support that reflected anger at the Muslim Brotherhood leader – who was democratically elected but failed to rule democratically. General Abdel Fatah al-Sisi pledged to follow a "road map" to democracy, but as repression continued the great hopes of Cairo's Tahrir Square in January 2011 were a distant memory.

Libya, scene of the only overt western intervention in the Arab uprisings, also faced multiple crises – not least the failure of the government in Tripoli to disarm autonomous militias. Its turmoil included the brief abduction of the prime minister and repeated strikes that paralysed the oil industry. Tunisia, where Islamists govern in coalition with other parties, has witnessed a growth in extremism but could still claim the prize for the smoothest transition from dictatorship to a functioning democracy.

For the region's oldest conflict, between Israelis and Palestinians, 2013 was a year of stasis. John Kerry, US secretary of state, embarked on a last-ditch push to broker an agreement by April 2014. Israeli anger over the Iran nuclear deal was a complication. Even without that, expanding Israeli settlements and the bitter divisions between the PLO in the West Bank and Hamas in Gaza seemed insurmountable barriers to an elusive breakthrough.

Hanging over everyone at year's end was a troubling question: is the US retreating from the Middle East? Obama's famous "pivot to Asia," the increasingly real prospect of US energy independence combined with Washington's evident reluctance to be drawn into new entanglements in an unpredictable area all suggest that the answer is a qualified yes.

Saudi Arabia certainly has reason to worry if, after 60 years, the US is losing its appetite for protecting the Strait of Hormuz just as Iran comes in from the cold and returns as a competitor to global oil markets. Israel without automatic US backing would be far less sure of itself. Neither of those changes looks like happening abruptly or any time soon. But the fact that question is in the air may concentrate minds and help forge new realities.